Documentation/Nightly/Modules/SubjectHierarchy - Revision history

Pinter: Removed all information, because everething moved to the Data module

2017-04-25T19:41:12Z

Removed all information, because everething moved to the Data module

Pinter at 14:12, 18 April 2017

2017-04-18T14:12:29Z

Pinter at 20:00, 30 March 2017

2017-03-30T20:00:07Z

Pinter at 20:23, 8 June 2016

2016-06-08T20:23:57Z

Pinter: Updated general module information

2016-06-08T20:21:16Z

Updated general module information

Pinter at 16:39, 18 May 2016

2016-05-18T16:39:10Z

Pinter: Updated subject hierarchy screenshot

2016-05-12T19:46:22Z

Updated subject hierarchy screenshot

Hillarylia: Fixed minor typos

2016-05-12T13:33:43Z

Fixed minor typos

Pinter: Added info about implementing new plugins

2016-01-21T17:55:38Z

Added info about implementing new plugins

Pinter at 17:13, 21 January 2016

2016-01-21T17:13:32Z

@@ Line 24: / Line 24: @@
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 {{documentation/{{documentation/version}}/module-section|Module Description}}
-The Subject hierarchy module acts as a central data-organizing point in Slicer. It shows all data nodes loaded into Slicer in an easy-to-explore way, and offers operations on the data nodes.<br>
+<big>'''The content of the Subject Hierarchy module moved to the [[Documentation/{{documentation/version}}/Modules/Data|Data module]]'''</big>
-DICOM data is automatically added as patient-study-series hierarchy. Non-DICOM data can be parsed if loaded from a local directory structure, or can be manually organized in tree structure by creating DICOM-like hierarchy or folders. Model hierarchies are automatically mirrored in subject hierarchy, so an atlas can be explored the usual way.<br><br>
+<br>
-Subject hierarchy provides features for the underlying data nodes, including cloning, bulk transforming, bulk show/hide, type-specific features, and basic node operations such as delete or rename. Additional plugins provide other type-specific features and general operations, see [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]
+<br>
+<br>
-<!-- ---------------------------- -->
+<br>
-{{documentation/{{documentation/version}}/module-section|Use Cases}}
+<br>
+<br>
-{|
+<br>
 <br>
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-footer}}
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@@ Line 26: / Line 26: @@
 The Subject hierarchy module acts as a central data-organizing point in Slicer. It shows all data nodes loaded into Slicer in an easy-to-explore way, and offers operations on the data nodes.<br>
 DICOM data is automatically added as patient-study-series hierarchy. Non-DICOM data can be parsed if loaded from a local directory structure, or can be manually organized in tree structure by creating DICOM-like hierarchy or folders. Model hierarchies are automatically mirrored in subject hierarchy, so an atlas can be explored the usual way.<br><br>
-Subject hierarchy node provides features for the underlying data nodes, including cloning, bulk transforming, bulk show/hide, type-specific features, and basic node operations such as delete or rename. Additional plugins provide other type-specific features and general operations, see [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]
+Subject hierarchy provides features for the underlying data nodes, including cloning, bulk transforming, bulk show/hide, type-specific features, and basic node operations such as delete or rename. Additional plugins provide other type-specific features and general operations, see [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]
 <!-- ---------------------------- -->

@@ Line 24: / Line 24: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-The Subject hierarchy module acts as a central data-organizing point in Slicer.<br><br>
+The Subject hierarchy module acts as a central data-organizing point in Slicer. It shows all data nodes loaded into Slicer in an easy-to-explore way, and offers operations on the data nodes.<br>
-It is deactivated by default, so when the user enters it the first time, it asks whether subject hierarchy should be created for the data loaded in Slicer. Clicking No leaves subject hierarchy unused, clicking Yes adds the nodes only once to subject hierarchy, and clicking Yes to All enables automtic creation of subject hierarchy nodes from all loaded data objects.<br><br>
+DICOM data is automatically added as patient-study-series hierarchy. Non-DICOM data can be parsed if loaded from a local directory structure, or can be manually organized in tree structure by creating DICOM-like hierarchy or folders. Model hierarchies are automatically mirrored in subject hierarchy, so an atlas can be explored the usual way.<br><br>
-DICOM data is automatically added as patient-study-series hierarchy. Non-DICOM data can be parsed if loaded from a local directory structure, or can be manually organized in tree structure by creating DICOM-like hierarchy or Folder nodes.<br><br>
+Subject hierarchy node provides features for the underlying data nodes, including cloning, bulk transforming, bulk show/hide, type-specific features, and basic node operations such as delete or rename. Additional plugins provide other type-specific features and general operations, see [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]
 <!-- ---------------------------- -->
@@ Line 53: / Line 52: @@
 * Data loaded from '''DICOM''' are automatically added to the tree in the right structure (patient, study, series)
 * '''Non-DICOM''' data also appears automatically in Subject hierarchy. There two ways are two ways to organize them in hierarchy
-** 'Create hierarchy '''from loaded directory structure'''' action in the context menu of the scene (see bottom screenshot). This organizes the nodes according to the local file structure they have been loaded from.
+** 'Create hierarchy '''from loaded directory structure'''' action in the context menu of the scene (right-click on empty area, see bottom screenshot). This organizes the nodes according to the local file structure they have been loaded from.
 ** Drag&drop manually under a hierarchy node
 * Nodes can be drag&dropped under other nodes, thus re-arranging the tree
 * Basic operations (accessible in the context menu of the nodes by right-clicking them)
@@ Line 64: / Line 64: @@
 ** '''Edit properties''': If the role of the node is specified (i.e. its icon is not a question mark), then the corresponding module is opened and the node selected (e.g. Volumes module for volumes)
 ** '''Create child...''': Create a node with the specified type
-* There are no nodes in the tree when Slicer is opened, new nodes can be added by right-clicking the Scene
+* There are no nodes in the tree when Slicer is opened, new nodes can be added by right-clicking the empty area (or the scene item if visible)
 * Roles and corresponding functions
 ** '''Volumes''': icon, Edit properties and additional information in tooltip
 *** ''''Register this...'''' action to select fixed image for registration. Right-click the moving image to initiate registration
-*** ''''Segment this using...'''' action allows segmenting the volume, for example, in the Editor module
+*** ''''Segment this...'''' action allows segmenting the volume, for example, in the Editor module
 *** ''''Toggle labelmap outline display'''' for labelmaps
 ** '''Models''': icon, Edit properties and additional information in tooltip
 ** '''SceneViews''': icon, Edit properties and Restore scene view
 ** '''Transforms''': icon, additional tooltip info, Edit properties, Invert, Reset to identity
-; MRML Node Inspector (closed drop-down panel under the tree)
+; Data MRML information (closed drop-down panel under the tree, visible if an item corresponding to a data node is selected)
-: Displays the attributes of the currently selected Subject hierarchy node. Can be edited by double-clicking on an attribute name or value
+: Displays the attributes of the data node corresponding to the currently selected subject hierarchy item. Attributes can be edited by double-clicking on an attribute name or value. The panel also shows detailed node information.
@@ Line 84: / Line 85: @@
 ; Create new Subject from scratch
-: Right-click on the top-level item 'Scene' and select 'Create new subject'
+: Right-click on the empty area and select 'Create new subject'
-; Create new hierarchy node
+; Create new folder
-: Right-click on an existing node and select 'Create child ...'. The type and level of the child node will be specified by the user and the possible types depend on the parent. Folder type hierarchy node can be converted to Subject or Study using the context menu
+: Right-click on an existing item or the empty area and select 'Create new folder'. Folder type hierarchy item can be converted to Subject or Study using the context menu
-; Rename Subject hierarchy node
+; Rename item
 : Right-click on the node and select 'Rename', or double-click the name of a node
@@ Line 111: / Line 112: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-* '''Important note''': Instead of the usual New function, vtkMRMLSubjectHierarchyNode::CreateSubjectHierarchyNode should be used for instantiating an SH node. The reason is that when SH auto creation is turned on, then there is no need to create an SH node, but only to set up its properties (parent, level, name, association), but when it is turned off, then creating an SH node is necessary if the module relies on it. The CreateSubjectHierarchyNode function takes care of this, and only creates a node if it doesn't exist, otherwise just updates its properties.
+* Code snippets accessing and manipulating subject hierarchy items can be found in the [https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Subject_hierarchy script repository]
 * '''Implementing new plugins''': Plugins are the real power of subject hierarchy, as they provide support for data node types, and add functionality to the context menu items.<br>To create a C++ plugin, implement a child class of qSlicerSubjectHierarchyAbstractPlugin, for Python plugin see below. Many examples can be found in Slicer core and in the SlicerRT extension, look for folders named SubjectHierarchyPlugins.
-** Role plugins: add support for new data node types
+** Writing plugins in '''Python''':
 *** Defines: ownership, icon, tooltip, edit properties, help text (in the yellow question mark popup), visibility icon, set/get display visibility, displayed node name (if different than name of the node object)
 *** Existing plugins in Slicer core: Markups, Models, SceneViews, Charts, Folder, Tables, Transforms, LabelMaps, Volumes
-** Function plugins: add feature in right-click context menu for certain types of nodes
+** '''Function''' plugins: add feature in right-click context menu for certain types of nodes
 *** Defines: list of contect menu actions for nodes and the scene, types of nodes for which the action shows up, functions handling the defined action
 *** Existing plugins in Slicer core: CloneNode, ParseLocalData, Register, Segment, DICOM
 * [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_naming_conventions Glossary of all the used terms in SlicerRT]

@@ Line 24: / Line 24: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-The {{documentation/modulename}} module acts as a central data-organizing point in Slicer.<br><br>
+The Subject hierarchy module acts as a central data-organizing point in Slicer.<br><br>
 It is deactivated by default, so when the user enters it the first time, it asks whether subject hierarchy should be created for the data loaded in Slicer. Clicking No leaves subject hierarchy unused, clicking Yes adds the nodes only once to subject hierarchy, and clicking Yes to All enables automtic creation of subject hierarchy nodes from all loaded data objects.<br><br>
 DICOM data is automatically added as patient-study-series hierarchy. Non-DICOM data can be parsed if loaded from a local directory structure, or can be manually organized in tree structure by creating DICOM-like hierarchy or Folder nodes.<br><br>

@@ Line 24: / Line 24: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-The {{documentation/modulename}} module acts as a central data-organizing point in Slicer. All DICOM data is automatically added to the tree. Non-DICOM data can be parsed if loaded from a local directory structure, or has to be manually added (non-SH nodes are the ones on the bottom with no icons).
+The {{documentation/modulename}} module acts as a central data-organizing point in Slicer.<br><br>
 Subject hierarchy nodes provide features for the underlying data nodes, including cloning, bulk transforming, bulk show/hide, type-specific features, and basic node operations such as delete or rename. Additional plugins can provide other type-specific features and general operations, see [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]

@@ Line 32: / Line 32: @@
 {|
+|
-* Load DICOM data and need to see in the same hierarchy
+* Overview all loaded data objects in the same place, types indicated by icons
 * Visualize and bulk-handle lots of data nodes loaded from disk
 * Easy show/hide of branches of displayable data
 * Transform whole study (any branch)
-* Export DICOM data (coming soon)
+* Export DICOM data (edit DICOM tags)
-* Edit DICOM tags (coming soon)
+* Lots of type-specific functionality offered by the plugins
 <!-- ---------------------------- -->

@@ Line 94: / Line 94: @@
+|
-[[File:20141116_SubjectHierarchyAnnouncement.png|thumb|536px| Subject hierarchy tree]]
+[[File:20160512_SubjectHierarchyScreenshot.png|thumb|425px| Subject hierarchy tree]]
 [[File:SlicerRT_0.13_HuntingtonsLongitudinalInSubjectHierarchy2.png|thumb|622px| Parse local data loaded from directory structures]]
 |}

@@ Line 105: / Line 105: @@
 {{documentation/{{documentation/version}}/module-section|References}}
 * Additional information on [[Documentation/Labs/SubjectHierarchy|Subject hierarchy labs page]]
-* Manual editing of contours can be done in the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Contours Contours module]
+* Manual editing of segmentations can be done in the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations module]
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